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Bioinformatics Tool for Prediction of Protein Solubility
Hronský, Patrik ; Burgetová, Ivana (referee) ; Martínek, Tomáš (advisor)
This master's thesis addresses the solubility of recombinant proteins and its prediction. It describes the subject of protein synthesis, as well as the process of recombinant protein creation. Recombinant protein synthesis is of great importance for example to pharmacologic industry. This synthesis is not a simple task and it does not always produce viable proteins. Protein solubility is an important factor, determining the viability of the resulting proteins. It is of course favourable for companies, that take part in recombinant protein synthesis, to focus their effort and their resources on proteins, that will be viable in the end. In this regard, bioinformatics is of great help, as it is capable, with the help of machine learning, of predicting the solubility of proteins, for example based on their sequences. This thesis introduces the reader to the basic principles of machine learning and presents several machine learning methods, used in the field of protein solubility prediction. It deals with the definition of a dataset, which is later used to test selected predictors, as well as to train the ensemble predictor, which is the main focus of this thesis. It also focuses on several specific protein solubility predictors and explains the basic principles upon which they are built, as well as the results of their testing. In the end, it presents the ensemble predictor of protein solubility.
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Processes of Nanoparticle Formation in Low Temperature Plasma
Brožek, V. ; Mastný, L. ; Moravec, Pavel ; Neufuss, Karel ; Ondráček, Jakub ; Ždímal, Vladimír
This work describes the synthesis of nanoparticles during interaction of several different metals (Ag) or their respective oxides (TiO2, Cr2O3) with oxygen-hydrogen plasma having temperatures above 25000 K. Resulting nanoparticles and/or their aggregates in the size range of 25-300 nm were deposited on metallic targets and/or trapped in the water filters and separated using ultra-centrifugal apparatus. The aerosol spectrometer SMPS 3936 (scanning mobility particle sizer) was used to study the particle size distribution of generated nanoparticles in the size range 14 – 700 nm. In order to extend the measured particle size range towards larger sizes, the APS 3321 spectrometer (aerodynamic particle sizer) with the size range 500-20000 nm was used simultaneously. Both spectrometers were set-up to sample with three minute time resolution. Process conditions and production of inorganic nanoparticles of defined composition are discussed in this work.
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Benzodiazine Derivatives as Compounds with Potential Bronchodilatory Activity
Šašková, Jaroslava ; Špulák, Marcel (advisor) ; Kuneš, Jiří (referee)
Charles University in Prague, Faculty of Pharmacy in Hradec Králové Department of Inorganic and organic chemistry Candidate Mgr. Jaroslava Šašková Consultant PharmDr. Marcel Špulák, PhD. Title of Thesis Benzodiazine derivatives as compounds with potential bronchodilatory activity This thesis describes the synthesis of various benzodiazines, in this case derived from quinazoline and quinoxaline. We followed a synthesis of quinazoline derivatives structurally analogous to vasicine and vasicinone, alkaloids isolated from a plant Adhatoda vasica. The original derivatives were tested by the common in vitro model of isolated rat trachea. Two compounds, 4-[3-(piperidine-1-yl)propyloxy]quinazoline and 4-[3-(piperidine-1-yl)propylsulfanyl]quinazoline, showed promising bronchodilatory activities. Therefore, we selected these molecules as model structures for our further syntheses. The first group of compounds was syntesized by oxidation of 4-[3-(piperidine-1-yl)propyloxy]quinazoline. We oxidated a nitrogen atom in the piperidine side chain of the parent molecule and we succeeded to create, in two steps, derivative based on quinazoline-1-oxide. Attempts to oxidize a sulphur atom in 4-[3-(piperidine-1-yl)propylsulfanyl]quinazoline were due to oxidative desulfuration unsuccessful, the only isolated product of...
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Study of Chemical Processes in Titan Atmosphere Initiated by Discharge in Electrode Configuration Like Gliding Arc Discharge
Töröková, Lucie ; Zahoranová, Anna (referee) ; Žabka,, Ján (referee) ; Krčma, František (advisor)
The aim of this work is the study of plasma processes and the synthesis of organic compounds due to electric discharge generated in gas mixture corresponding to the composition of the atmosphere of Saturn's largest moon Titan. This study focuses on the mimic of Titan's atmosphere at atmospheric pressure and ambient laboratory temperature. The chemical composition of Titan's atmosphere is very similar to atmosphere of prehistoric Earth. Many articles have been published with theoretical model-research, and laboratory experiments are the pursuit of their interconnection. The main aim of thesis is the identification of synthesized gaseous organic, amino, imino and cyano compounds by use to various analytical methods such as the PTR-MS, FTIR and GC-MS. The OES and electric measurements were applied to the determination of selected electric discharge parameters. The gaseous products and radicals formed in an atmospheric discharge fed by different mixtures of N2:CH4 (0,5 up to 5 % of CH4) operated in a flowing regime at the total gas mixture flows from 50 to 200 sccm at different discharge currents from 15 up to 40 mA were determined. A part of experiments was carried out with admixtures of CO2 and hydrogen. This first part of results has been obtained using OES in dependence on the gas mixture composition and supplied power. The bands of the nitrogen second positive and the first negative systems, CN violet system and Swan system of C2 were recorded. Besides them, atomic lines H, H, and C (in the second order) were also observed. These spectra allowed calculation of rotational and vibrational temperatures. FTIR in situ analysis of the gaseous products showed presence of various nitrile compounds and hydrocarbons in all experiments. The HCN, C2H2, NH3 were the main products generated in our system. The dependences of their concentrations on various experimental parameters were measured. The other part of this work was devoted to estimate the influence of CO2 traces addition on the reactivity in the gaseous mixtures mentioned above. Besides the main products mentioned above, CO2 and CO were detected and also some more complicated oxygen molecules has been confirmed but not estimated because of FTIR spectra complexity. In the case of hydrogen traces addition into the reaction gas mixture, no other compounds were determined. Impurities of CO2 as well as hydrogen have a great positive influence on the production efficiency of the major generated compounds at all conditions. The more detailed gaseous products analyses were carried out using the in situ PTR-MS. A huge number of different molecular structures containing nitrile groups (–CN), amino groups (–NH2, –NH–, –N CH3CN > C2H5CN. Besides them, many other hydrocarbons and nitriles were detected. Presence of all compounds was studi
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Cyclization Reactions Mediated by Transition Metals
Matoušová, Eliška ; Pour, Milan (advisor) ; Bureš, Filip (referee) ; Šrogl, Jiří (referee)
Charles University in Prague, Faculty of Pharmacy in Hradec Králové Department of inorganic and organic chemistry Candidate: Mgr. Eliška Matoušová Supervisor: prof. RNDr. Milan Pour, PhD. Title of Doctoral Thesis: Cyclization reactions mediated by transition metals Within the framework of this Thesis, several analogues of naturally occurring biologically active pyranones were prepared. The synthetic procedure was based on a Pd-cata- lyzed carbopalladation of enyne precursors with subsequent lactonization. Employing this method, bicyclic pentenolides containing fused nitrogen heterocycle as well as carbocycle were synthesized. The preparation of the corresponding oxygen-containing derivative was not successful. The compounds were tested for their antifungal, anitibacterial and cytostatic activity. The second part of the Thesis deals with synthesis of furans and dihydropyrans via palladium and gold catalysis. A highly efficient method for AuI -catalyzed cyclization of propargyl vinyl ethers to dihydropyrans was developed using tris(2-furyl)phosphine as a ligand and methanol as a nucleophile. This method was employed for the preparation of 15 dihydropyran derivatives in high yields. In the absence of a nucleophile furans were formed in lower yields. Dihydropyrans undergo an as yet undescribed...
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Rheological properties of gels for Pechini syntheses
Wirthová, Michaela ; Ptáček, Petr (referee) ; Zmrzlý, Martin (advisor)
This work deals with preparation of layers of ceramic materials – perovskites. The introductory part includes general characteristics concerning structure, properties and use of this materials. In details then there is described method of their preparation, namely Pechini´s syntheses, which are most widely used. Optimum molar ratio of components is discussed, in the sense of what compositions lead to creation of perovskite structures. Influence of this parameter on rheological properties of precursory gels is described in the end of the first part of work. In experimental section there are described preparations of gels, which are prepared via reaction between citric acid and ethylene glycol and gels, which are prepared by Pechini´s synthesis. Rheological properties of prepared gels (density, viscosity and surface tension) and besides determination of amount of nitrates in gels are characterized. Temperature dependence of viscosity of gels, that are prepared by reaction of citric acid and ethylene glycol are determined. In final part successful preparations of perovskite layers is shown on ceramic substrate. This layers are observed by means of light optical microscope and scanning electron microscope.
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Influence of extracellular matrix environment on gene expression in liver myofibriloblasts
Jiroutová, Alena ; Kanta, Jiří (advisor) ; Ehrmann, Jiří (referee) ; Sedláček, Radislav (referee)
Influence of extracellular matrix environment on gene expression in liver myofibroblast (summary) Hepatic stellate cells (HSC) and liver myofibroblasts (MF) are two cell populations most likely responsible for the synthesis of majority of connective tissue components in fibrotic liver. They differ in their origin and location in the liver, and in the spectrum of genes they express. HSC are located in Disse spaces of normal rat liver around the sinusoids, in fibrotic liver they become activated, proliferate and they undergo transdifferentiation into myofibroblast-like cells. Myofibroblasts are heterogenous cell population that consists at least of portal pMF, septal sMF and interface iMF. pMF, which are adjacent to bile duct epithelia, may be a mediator of billiary type fibrosis. sMF are located within and along the collagenous septum in cirrhotic liver. Little is known about the expression of genes involved in connective tissue metabolism in MF cultured in fibrin or collagen gels that more closely resemble natural cell environment. Fibrin is deposited in liver at sites of injury and collagen type I forms a substantial part of fibrotic septa. In our study oligo cDNA array analysis was used to determine gene expression in quiescent HSC, activated HSC and MF isolated from both normal and CCl4-cirrhotic liver....
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Taxonomy and variability of selected Sorbus taxa
LEPŠÍ, Martin
This thesis is a biosystematic study focusing on the taxonomy and variability of selected taxa of the genus Sorbus, one of the most diverse and taxonomically complicated plant groups in Europe. Classical and modern biosystematic methods - comparative study, chromosome counting, analysis of nuclear microsatellite markers, flow cytometry, and traditional multivariate and outline morphometric analyses were used to assess the morphological, karyological and genetic variability of the genus. The final synthesis of these approaches led to the description of several new taxa (species, hybrids and a subgenus) and the correction of several taxonomic misinterpretations. To reveal ongoing evolutionary processes responsible for the generation of the observed variability, the reproductive modes of 42 Sorbus taxa were examined using flow-cytometric seed and pollen screens. Apart from revealing major trends, the study estimates the frequency of rare events and provides several novel conclusions that are relevant both specifically to Sorbus/Rosaceae and to apomixis in general.
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Synthesis and Characterization of Multifunctionalized Biodegradable Copolymers
Michlovská, Lenka ; Petrůj, Jaroslav (referee) ; Lehocký,, Marián (referee) ; Vojtová, Lucy (advisor)
Předložená disertační práce shrnuje současné poznatky v oblasti termosenzitivních biodegradabilních kopolymerů, které ve formě vodného solu gelují při teplotě lidského těla. Tyto polymerní materiály jsou použitelné v medicíně pro injekční aplikace jako nosiče léčiv či resorbovatelné implantáty pro regeneraci tkání. V experimentální práci byly pomocí vakuové linky syntetizovány termosenzitivní amfifilní triblokové kopolymery na bázi biodegradabilního hydrofobního polylaktidu a polyglykolidu a biokompatibilního hydrofilního polyethylenglykolu (PLGA–PEG–PLGA). Připravený PLGA–PEG–PLGA kopolymer se dvěma fázovými přechody sol-gel a gel-suspenze byl následně modifikován anhydridem kyseliny itakonové. Výsledný funkcionalizovaný ITA/PLGA–PEG–PLGA/ITA kopolymer obsahuje na koncích řetězců reaktivní dvojné vazby vhodné k další polymeraci či síťování a karboxylové skupiny pro případné modifikace biologicky aktivními látkami. Fyzikální i chemické síťování bylo dále sledováno jak z hlediska poměrů hydrofilního a hydrofobního řetězce, tak i z hlediska množství navázané kyseliny itakonové. Vodné roztoky syntetizovaného ITA/PLGA–PEG–PLGA/ITA kopolymeru gelují v rozmezí teplot 33 - 43 °C. Kritická gelační koncentrace byla 6 % a kritická gelační teplota 34 °C pro kopolymer s poměrem PLGA/PEG = 2,5. Čím je kopolymer více hydrofobní, tím geluje dříve a je více hydrolyticky stabilní. Tuhost gelu stoupá se zvyšujícím se poměrem PLGA/PEG a je závislá na typu rozpouštědla použitého při přečišťování kopolymeru. Připravené ITA/PLGA–PEG–PLGA/ITA makomonomerů byly síťovány pomocí modrého světla bez dalšího síťovadla. Hydrolytická stabilita vzorků modifikovaných pomocí ITA se výrazně zlepšila a zvýšila v přímé úměře jak s rostoucí dobou síťování, tak s množstvím dvojných vazeb na koncích řetězců. Vzorek s 63 mol% ITA síťovaný 40 minut ve vodě zcela zdegradoval po 32 dnech. Protonovou NMR relaxometrií bylo zjištěno, že když vzorek ve vodě nabotnal (po cca 12 hodinách), množství nevázané vody se začalo snižovat a postupně difundovat do kavit na povrchu vzorku a pomalu se měnit na slabě a pevně vázanou vodu na polymerní řetězce. Nicméně, termální stabilita chemicky síťovaných vzorků vzrůstala pouze do 20 minut síťování. Pomocí ATR-FTIR bylo prokázáno, že se přibližně 57 % dvojných vazeb kyseliny itakonové (při vlnové délce 1640 cm-1) přeměnilo na nové jednoduché RR'C-CHR'' vazby při vlnové délce 795 cm-1. Delší čas síťování (nad 30 minut) vedl ke změnám v chemické struktuře pomocí beta-štěpení řetězců a částečné rekombinaci dvojných vazeb. Díky vzniku nových dvojných vazeb v jiných částech řetězce se snížila termální stabilita z 242 °C na 237° C a teplota skelného přechodu z -2,2 na -5.8 °C. Předložená práce popisuje, jak složení polymeru, modifikace funkčními skupinami a fyzikální podmínky ovlivňují fyzikální a chemické síťování připravených amfifilních kopolymerů. Kontrola hydrolytické a termální stability hydrogelů je zapotřebí zejména při uvolňování léčiv a regeneraci tkání.
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The Synthesis and Characterisation of Biocomposite Materials for Potential Application in Medicine
Balgová, Zuzana ; Plešingerová,, Beatrice (referee) ; Bakoš, Dušan (referee) ; Palou, Martin (advisor)
Dizertační práce se zabývala syntézou a studiem kompozitních materiálů pro potenciální lékařské využití. Teoretická část je zaměřena na biomateriály, zejména na kompozity složené z polyvinylalkoholu a hydroxyapatitu(PVA/HA). Byly připraveny kompozitní membrány složené z polyvinylalkoholu s různým hmotnostním zastoupením hydroxyapatitu - 0%, 10%, 20%, 30%, 40% a 50%. Hydroxyapatit (HA) byl připraven srážecí metodou z hydrogenfosforečnanu amonného a tetrahydrátu dusičnanu vápenatého ve vodném alkalickém prostředí. Vzniklá suspenze se smísila s roztokem polyvinylalkoholu, který byl připraven rozpuštěním ve vodě o teplotě 85° C. Jednotlivé směsi byly odlity do formy a sušeny po dobu 7 dní při teplotě 30 ° C, vzniklé 0,5 mm tenké membrány byly analyzovány ATR-FTIR spektroskopií k identifikaci funkčních skupin v kompozitu, dále byla provedena XRD analýza. Zkouška tahem a TGA měření byly realizovány k určení vlivu HA na mechanické vlastnosti, respektive změnu tepelné odolnosti kompozitů ve srovnání s čistým PVA. Byla provedena zkouška bioaktivity v simulovaném krevním roztoku (SBF) po dobu 2h, 7 a 28 dnů. SEM byla použita k charakterizaci povrchové mikrostruktury biocompositních membrán před a po ponoření do SBF. Na povrchu testovaných membrán vznikla vrstva apatitu, která je charakteristická pro bioaktivní materiály. Bylo zjištěno, že s rostoucím množstvím HA částic docházelo ke vzniku aglomerátů v kompozitu, které vznikly mimo jiné jako důsledek růstu krystalů HA během sušení membrán. Bioaktivita rostla s delším působením SBF na vzorky.
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